FMN2 p.Pro957=
c.2871C>T · rs529662001 · VCV3036961
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0371%, amr)
Conditions
1
FMN2-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -20 | GERP -2.1 |
| Overall | ||
| CADD | 1.994 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0371%
Admixed American · 21/56,576 alleles
Filtering AF
0.0249%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0208%
Overall
0.00454%
65/1,430,760 alleles · ultra-rare
exomes 58/1,290,066 · genomes 7/140,694 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0371% | 2,694 |
| Remaining individualsnot grpmax-eligible | 0.00542% | 18,441 |
| European (non-Finnish) | 0.00377% | 26,550 |
| African / African-American | 0.003% | 33,280 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- FMN2
- Protein
- p.Pro957=
- Coding
- c.2871C>T
- MANE Select
- NM_020066
- dbSNP
- rs529662001
- Type
- single nucleotide variant
- Location
- chr1:240207683 (GRCh38)
- Gene constraint
- LOEUF 0.51 · pLI 0.51 (gnomAD)
- Structure
- AlphaFold pLDDT 51.48 · 2 PDB
- Residue 957
- the fh1 domain; the 'disordered' region
Disease context
FMN2-related disorder
Similar variants
- FMN2 p.Ala951= Likely benign ★★ same condition
- FMN2 p.Ala973= Benign/Likely benign ★★ same condition
- FMN2 p.Gly1005= Likely benign ★★ same condition
- FMN2 p.Gly1007= Likely benign ★★ same condition
- FMN2 p.Gly1062= Likely benign ★★ same condition
- FMN2 p.Gly941= Likely benign ★★ same condition
- FMN2 p.Leu1058= Likely benign ★★ same condition
- FMN2 p.Leu1069= Likely benign ★★ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/fmn2-p-pro957 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown